It was shown recently (Calvez et al. 2007) that glpQ and pde genes are involved in intermediate resistance of Enterococcus faecalis JH2-2 to DvnV41, a class IIa bacteriocin produced by Carnobacterium divergens V41. The listerial orthologs of lpQ and pde genes might be lmo0052 and lmo1292 genes, respectively. Here, the role of lmo0052 and lmo1292 genes in resistance of Listeria monocytogenes EGDe to DvnV41 and MesY105 was investigated. L. monocytogenes EGDe was inactivated in lmo0052 and/or lmo1292 by homologous recombination. Listerial mutant strain EGDSC02 (inactivated in the putative glpQ gene), was slightly resistant to DvnV41. The listerial mutant strain EGDSC01 (inactivated in the putative pde gene) remained, as the wild-type strain, sensitive to DvnV41, but was affected in growth parameters.

• MeSH
• Anti-Bacterial Agents pharmacology   MeSH
• Drug Resistance, Bacterial MeSH
• Bacterial Proteins genetics   drug effects   MeSH
• Bacteriocins biosynthesis   pharmacology   MeSH
• Phosphoric Diester Hydrolases genetics   drug effects   MeSH
• Listeria monocytogenes genetics   growth & development   drug effects   MeSH
• Microbial Sensitivity Tests MeSH
• Mutation MeSH

• MeSH
• Bacteriocins isolation & purification   MeSH
• Chromatography, Affinity methods   utilization   MeSH
• DNA genetics   classification   MeSH
• Enzyme-Linked Immunosorbent Assay methods   utilization   MeSH
• Enterococcus faecalis enzymology   genetics   MeSH
• Escherichia coli genetics   immunology   MeSH
• Financing, Government MeSH
• Humans MeSH
• Polymerase Chain Reaction methods   utilization   MeSH
• Check Tag
• Humans MeSH

When patterns are set during embryogenesis, it is expected that they are straightly established rather than subsequently modified. The patterning of the three mouse molars is, however, far from straight, likely as a result of mouse evolutionary history. The first-formed tooth signaling centers, called MS and R2, disappear before driving tooth formation and are thought to be vestiges of the premolars found in mouse ancestors. Moreover, the mature signaling center of the first molar (M1) is formed from the fusion of two signaling centers (R2 and early M1). Here, we report that broad activation of Edar expression precedes its spatial restriction to tooth signaling centers. This reveals a hidden two-step patterning process for tooth signaling centers, which was modeled with a single activator-inhibitor pair subject to reaction-diffusion (RD). The study of Edar expression also unveiled successive phases of signaling center formation, erasing, recovering, and fusion. Our model, in which R2 signaling center is not intrinsically defective but erased by the broad activation preceding M1 signaling center formation, predicted the surprising rescue of R2 in Edar mutant mice, where activation is reduced. The importance of this R2-M1 interaction was confirmed by ex vivo cultures showing that R2 is capable of forming a tooth. Finally, by introducing chemotaxis as a secondary process to RD, we recapitulated in silico different conditions in which R2 and M1 centers fuse or not. In conclusion, pattern formation in the mouse molar field relies on basic mechanisms whose dynamics produce embryonic patterns that are plastic objects rather than fixed end points.

• MeSH
• Models, Biological * MeSH
• Chemotaxis MeSH
• Epithelium embryology   metabolism   MeSH
• Mice, Mutant Strains MeSH
• Mice MeSH
• Edar Receptor genetics   metabolism   MeSH
• Body Patterning * MeSH
• Signal Transduction * MeSH
• Hair embryology   MeSH
• Gene Expression Regulation, Developmental MeSH
• Tooth Germ embryology   metabolism   MeSH
• Tooth embryology   metabolism   MeSH
• Animals MeSH
• Check Tag
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

• MeSH
• Herpesviridae immunology   blood   MeSH
• HIV Infections complications   MeSH
• Homosexuality, Male MeSH
• Humans MeSH
• Prevalence MeSH
• Antibodies, Viral MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Geographicals
• Slovakia MeSH

Gene expression microarray and next generation sequencing efforts on conventional, clear cell renal cell carcinoma (ccRCC) have been mostly performed in North American and Western European populations, while the highest incidence rates are found in Central/Eastern Europe. We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients recruited within the "K2 Study", using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of this cancer. Differential expression analysis identified 1650 significant probes (fold change ≥2 and false discovery rate <0.05) mapping to 630 up- and 720 down-regulated unique genes. We performed similar statistical analysis on the RNA sequencing data of 65 ccRCC cases from the Cancer Genome Atlas (TCGA) project and identified 60% (402) of the downregulated and 74% (469) of the upregulated genes found in the K2 series. The biological characterization of the significantly deregulated genes demonstrated involvement of downregulated genes in metabolic and catabolic processes, excretion, oxidation reduction, ion transport and response to chemical stimulus, while simultaneously upregulated genes were associated with immune and inflammatory responses, response to hypoxia, stress, wounding, vasculature development and cell activation. Furthermore, genome-wide DNA methylation analysis of 317 TCGA ccRCC/adjacent non-tumour renal tissue pairs indicated that deregulation of approximately 7% of genes could be explained by epigenetic changes. Finally, survival analysis conducted on 89 K2 and 464 TCGA cases identified 8 genes associated with differential prognostic outcomes. In conclusion, a large proportion of ccRCC molecular characteristics were common to the two populations and several may have clinical implications when validated further through large clinical cohorts.

• MeSH
• Survival Analysis MeSH
• Adult MeSH
• Carcinoma, Renal Cell genetics   mortality   pathology   MeSH
• Middle Aged MeSH
• Humans MeSH
• DNA Methylation MeSH
• Kidney Neoplasms genetics   mortality   pathology   MeSH
• Prognosis MeSH
• Oligonucleotide Array Sequence Analysis MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Gene Expression Profiling MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged, 80 and over MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Geographicals
• Czech Republic MeSH
• United States MeSH

BACKGROUND: The DNA released into the bloodstream by malignant tumours· called circulating tumour DNA (ctDNA), is often a small fraction of total cell-free DNA shed predominantly by hematopoietic cells and is therefore challenging to detect. Understanding the biological properties of ctDNA is key to the investigation of its clinical relevance as a non-invasive marker for cancer detection and monitoring. METHODS: We selected 40 plasma DNA samples of pancreatic cancer cases previously reported to carry a KRAS mutation at the 'hotspot' codon 12 and re-screened the cell-free DNA using a 4-size amplicons strategy (57 bp, 79 bp, 167 bp and 218 bp) combined with ultra-deep sequencing in order to investigate whether amplicon lengths could impact on the capacity of detection of ctDNA, which in turn could provide inference of ctDNA and non-malignant cell-free DNA size distribution. FINDINGS: Higher KRAS amplicon size (167 bp and 218 bp) was associated with lower detectable cell-free DNA mutant allelic fractions (p < 0·0001), with up to 4·6-fold (95% CI: 2·6-8·1) difference on average when comparing the 218bp- and the 57bp-amplicons. The proportion of cases with detectable KRAS mutations was also hampered with increased amplicon lengths, with only half of the cases having detectable ctDNA using the 218 bp assay relative to those detected with amplicons less than 80 bp. INTERPRETATION: Tumour-derived mutations are carried by shorter cell-free DNA fragments than fragments of wild-type allele. Targeting short amplicons increases the sensitivity of cell-free DNA assays for pancreatic cancer and should be taken into account for optimized assay design and for evaluating their clinical performance. FUNDING: IARC; MH CZ - DRO; MH SK; exchange program between IARC and Sao Paulo medical Sciences; French Cancer League.

• MeSH
• Alleles MeSH
• Pancreatitis, Chronic blood   diagnosis   genetics   pathology   MeSH
• Circulating Tumor DNA blood   genetics   MeSH
• Gene Expression MeSH
• Gene Frequency MeSH
• Codon MeSH
• Humans MeSH
• Mutation MeSH
• Biomarkers, Tumor blood   genetics   MeSH
• Pancreatic Neoplasms blood   diagnosis   genetics   pathology   MeSH
• Proto-Oncogene Proteins p21(ras) blood   genetics   MeSH
• Base Sequence MeSH
• Sensitivity and Specificity MeSH
• Case-Control Studies MeSH
• Computational Biology MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Multicenter Study MeSH

The utility of KRAS mutations in plasma circulating cell-free DNA (cfDNA) samples as non-invasive biomarkers for the detection of pancreatic cancer has never been evaluated in a large case-control series. We applied a KRAS amplicon-based deep sequencing strategy combined with analytical pipeline specifically designed for the detection of low-abundance mutations to screen plasma samples of 437 pancreatic cancer cases, 141 chronic pancreatitis subjects, and 394 healthy controls. We detected mutations in 21.1% (N=92) of cases, of whom 82 (89.1%) carried at least one mutation at hotspot codons 12, 13 or 61, with mutant allelic fractions from 0.08% to 79%. Advanced stages were associated with an increased proportion of detection, with KRAS cfDNA mutations detected in 10.3%, 17,5% and 33.3% of cases with local, regional and systemic stages, respectively. We also detected KRAS cfDNA mutations in 3.7% (N=14) of healthy controls and in 4.3% (N=6) of subjects with chronic pancreatitis, but at significantly lower allelic fractions than in cases. Combining cfDNA KRAS mutations and CA19-9 plasma levels on a limited set of case-control samples did not improve the overall performance of the biomarkers as compared to CA19-9 alone. Whether the limited sensitivity and specificity observed in our series of KRAS mutations in plasma cfDNA as biomarkers for pancreatic cancer detection are attributable to methodological limitations or to the biology of cfDNA should be further assessed in large case-control series.

• MeSH
• CA-19-9 Antigen blood   MeSH
• Circulating Tumor DNA blood   genetics   MeSH
• Carcinoma, Pancreatic Ductal blood   genetics   pathology   MeSH
• Phenotype MeSH
• Gene Frequency MeSH
• Genetic Predisposition to Disease MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation * MeSH
• DNA Mutational Analysis MeSH
• Biomarkers, Tumor blood   genetics   MeSH
• Pancreatic Neoplasms blood   genetics   pathology   MeSH
• Pilot Projects MeSH
• Predictive Value of Tests MeSH
• Proto-Oncogene Proteins p21(ras) blood   genetics   MeSH
• Reproducibility of Results MeSH
• Aged MeSH
• Neoplasm Staging MeSH
• Case-Control Studies MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Multicenter Study MeSH
• Validation Study MeSH
• Geographicals
• Czech Republic MeSH
• Slovakia MeSH

The use of non-invasive biomarkers such as circulating tumor DNA (ctDNA) in head and neck tumors may be of relevance in early diagnosis and eventually improved outcome. We evaluated two different approaches from two case series in Europe and South America including (i) targeted screening of ctDNA mutations, and (ii) detection of TP53 mutations in plasma and oral rinses without previous knowledge of mutational status in tumor samples. Targeted sequencing in 5 genes identified ctDNA mutations in plasma among 42% of HNSCC cases, 67% of who were early stage cases. No association was found between ctDNA mutation detection and overall survival. Sequencing of the entire coding region of the TP53 gene resulted in identification of TP53 mutations in 76% of tumor cases. However, concordance of mutation detection was low between tumor, oral rinses (11%) and plasma (2,7%) samples. Identification of 5 pathogenic TP53 mutations in oral rinses from 3 non-cancer controls gives additional evidence of mutation occurrence in individuals without a diagnosed cancer and presents an additional challenge for the development of ctDNA diagnostic assays.

• Publication type
• Journal Article MeSH

We investigated how somatic changes in HNSCC interact with environmental and host risk factors and whether they influence the risk of HNSCC occurrence and outcome. 180-paired samples diagnosed as HNSCC in two high incidence regions of Europe and South America underwent targeted sequencing (14 genes) and evaluation of copy number alterations (SCNAs). TP53, PIK3CA, NOTCH1, TP63 and CDKN2A were the most frequently mutated genes. Cases were characterized by a low copy number burden with recurrent focal amplification in 11q13.3 and deletion in 15q22. Cases with low SCNAs showed an improved overall survival. We found significant correlations with decreased overall survival between focal amplified regions 4p16, 10q22 and 22q11, and losses in 12p12, 15q14 and 15q22. The mutational landscape in our cases showed an association to both environmental exposures and clinical characteristics. We confirmed that somatic copy number alterations are an important predictor of HNSCC overall survival.

• MeSH
• Survival Analysis MeSH
• Adult MeSH
• Incidence MeSH
• Middle Aged MeSH
• Humans MeSH
• Chromosomes, Human MeSH
• Adolescent MeSH
• Young Adult MeSH
• Head and Neck Neoplasms epidemiology   genetics   MeSH
• Aged MeSH
• DNA Copy Number Variations MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Sexual dimorphism in cancer incidence and outcome is widespread. Understanding the underlying mechanisms is fundamental to improve cancer prevention and clinical management. Sex disparities are particularly striking in kidney cancer: across diverse populations, men consistently show unexplained 2-fold increased incidence and worse prognosis. We have characterized genome-wide expression and regulatory networks of 609 renal tumors and 256 non-tumor renal tissues. Normal kidney displayed sex-specific transcriptional signatures, including higher expression of X-linked tumor suppressor genes in women. Sex-dependent genotype-phenotype associations unraveled women-specific immune regulation. Sex differences were markedly expanded in tumors, with male-biased expression of key genes implicated in metabolism, non-malignant diseases with male predominance and carcinogenesis, including markers of tumor infiltrating leukocytes. Analysis of sex-dependent RCC progression and survival uncovered prognostic markers involved in immune response and oxygen homeostasis. In summary, human kidney tissues display remarkable sexual dimorphism at the molecular level. Sex-specific transcriptional signatures further shape renal cancer, with relevance for clinical management.

• MeSH
• Genome-Wide Association Study MeSH
• Genetic Predisposition to Disease * MeSH
• Genetic Association Studies MeSH
• Genes, X-Linked MeSH
• Carcinoma, Renal Cell genetics   metabolism   MeSH
• Middle Aged MeSH
• Humans MeSH
• Biomarkers, Tumor metabolism   MeSH
• Kidney Neoplasms genetics   metabolism   MeSH
• Sex Characteristics * MeSH
• Prognosis MeSH
• Disease Progression MeSH
• Gene Expression Regulation, Neoplastic * MeSH
• Aged MeSH
• Gene Expression Profiling * MeSH
• Genes, Tumor Suppressor MeSH
• Check Tag
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH